ARCHIVES - Deep Gene in the News
- National Geographic June 4th, 2001
- A news brief about the evolution of all multicellular land
plants from only one lineage of algae, even though three other
algal lineages made the transition from water to land. Commentary
by UC Berkeley's Brent Mishler and Louisiana State's Russell
- The Advocate ONLINE May 29, 2001
- Article on Cephaleuros, Magnolias, and Deep Green/Deep Gene
by Marlene Naanes
- The Scientist 15:12, March 5, 2001
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to view this article ***
- 'Deep Gene' and 'Deep Time' Evolving collaborations parse
the plant family tree by Barry A. Palevitz
- Financial Times March 3, 2001
- The Nature of Things: A project to unravel the ancestry of
today's flora has produced a surprise by Clive Cookson
- Science Online Febuary 19, 2001***
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- Invasions of the Algae; green algae and Deep Gene, by Jay
- UC Berkeley Press Release Febuary 16,
- Deep Green spawns Deep Gene and Deep Time... by Robert Sanders
- NSF News January 31, 2001
- Scientists Shake Up "Family Tree" of Green Plants
|National Geographic June 4th, 2001 [top]
|All Land Plants Evolved From Single Type of Algae, Scientists
Charleston Daily Mail
June 4, 2001
The first tentative moves that got life out of the water and
onto the land eons ago were apparently made by slimy green algae,
scientists say, and coming ashore wasn't easy.
According to paleobotanist Russell Chapman of Louisiana State
University, the first algae that managed to gain residence on
terra firma-finally kick-starting the evolution of land plants-must
have come out of fresh water, not the sea.
And, Chapman said, even though four distinct types of algae managed
to come ashore, only one of them evolved enough complexity to
eventually cover the land with vegetation, what we now call trees,
shrubs, flowers, and grass. Nonetheless, all four species of pioneering
algae can still be found on land, he said.
The ancient history of land plants is becoming evident because
of recent advances in techniques for genetic analysis. It's now
possible to look at individual genes in algal cells and higher
plants and calculate their similarity. Clues to the history of
such organisms lie within the chemical "spelling"-the
sequence similarity-of the organisms' genes. The closer they resemble
each other, the closer they are related.
"The evolutionary history of various genes can be studied
within the lineage of green algae," Chapman said, and that
is what offers vital clues to how the algal genes eventually evolved
to produce plants. Today's green plants are enormously varied,
from the giant redwood trees to the tiniest weeds-everything that
blooms, including our crops.
All Plants Rose From Single Type of Algae
Chapman was speaking earlier this year during a symposium on
the genetics and evolution of green plants at the annual meeting
of the American Association for the Advancement of Science in
San Francisco. He and several colleagues made it clear that today's
multicellular plants, such as corn, cabbages and all the other
greenery, arose from a single type of algae.
As noted by plant geneticist Brent Mishler of the University
of California at Berkeley, the genetic evidence now being uncovered
shows that "the multicellular land plants are all of one
lineage. The fossil evidence suggests that others (types of algae)
tried," but they failed to evolve the needed complexity.
In other words, the three other algae that managed to wade ashore
didn't evolve beyond the single-cell stage, so they remain what
they were, algae.
The discoveries and the ideas of how land plants arose "reminds
people of our humble origins," Chapman added. "This
reminds people of how important algae are in general, since without
that one escape from water and subsequent evolution, the half
million species of plants that are so important to life on Earth
might not exist. There would be no crops, no flowers, no fibers
or foods. Also no us, of course."
(C) 2001 Charleston Daily Mail
|The Advocate ONLINE May 29, 2001 [top]
In the summer, the creamy-white flowers of thousands of magnolia
trees in yards and wilderness areas across the state emit a rich
The magnolia became the state flower in 1900 because of its abundance
in Louisiana. Scientists then did not know the flower had more
to offer than beauty and fragrance. Its leaves also offer a clue
to the past that would later let scientists look back into the
history of land plants about 500 million years ago.
The key to the past is an alga that lives on the leaves of the
magnolia tree. Cephaleuros virescens is a species of green alga
which contains an orange pigment that grows on the leaves, resembling
an orange, velvety disc.
The significance of that alga is that it came from algae that
originated in marine, or salty, water about 500 million to 600
million years ago, which made it a contender for the title of
first form of green life on earth.
However, freshwater algae endured foreign environmental conditions
hundreds of millions of years ago, which shifted their preferred
environment from water to land.
Those freshwater algae not only became the only form of green
life on land at that time, they also gave rise to every form of
green life on the Earth today, including Louisiana's magnolia
A professor and researcher at LSU, Russell Chapman, studied the
origins of green plants with about 200 researchers around the
world in a project called Deep Green.
The project answered questions about the evolution of green plants,
including the possible species that gave rise to all land plants.
"Understanding the evolution of green plants is important
because plants are so important," said Chapman, executive
director of the Center for Coastal, Energy and Environmental Resources.
"We use plants for food, medicines and shelter."
The project, which just wrapped up this year, revealed that all
land plants come from a single line of freshwater green algae
called Charophyceae. Scientists determined these algae were the
origin of all plants after the scientists performed rounds of
tests on the alga's DNA, cell division processes and morphology.
Before the Deep Green project, scientists did not know the algal
key players in the evolution of all land plants.
Chapman's research assistant, Debra Waters, equates the discovery
of Charophyceae to finding the missing link in human evolution
The discovery was also interesting because it had seemed more
likely that the origin of all plants was a marine alga. Some marine
algae have the ability to alter life processes to survive harsh
environments. Every time a tide rises or falls, their living conditions
Since the move from water to land would create harsh conditions
for a water alga, a marine alga that could alter its life processes
was more fit for a move than a freshwater alga.
Yet, the freshwater algae prevailed as the original land dwelling
plant, much to the fascination of Chapman and Waters.
Deep Green also provided critical genetic information by outlining
a genealogy of plants and algae.
The plant family tree not only revealed the evolution of green
plants, but detailed some aspects of plant and algal genetic layout.
It also detailed the organisms' biological processes, which will
allow scientists to compare species.
A project that generates that much information is significant
for several reasons, including getting questions answered before
any more plants become extinct, Chapman said.
"If a certain plant is known to produce a helpful compound,
it's helpful to know of a related plant," Chapman said. "Because
if the (original) plant doesn't grow well, you can see if relatives
have a similar compound."
Deep Green research also can be applied to genetic engineering
of crop plants, he said.
"Knowing how certain structures and processes evolved could
help us learn how to improve them," he said.
Scientists may be able to control when a crop plant will produce
leaves or flowers using the genetic information from Deep Green,
said Linda Graham, a professor of botany and environmental studies
at the University of Wisconsin-Madison who was also involved in
Controlling growth of a plant will also control when it produces
its edible portion, Graham said.
Scientists, now knowing which genes evolved to produce certain
proteins in plants, can use that information to engineer a plant
to produce more of that protein, Chapman said.
Though Deep Green answered some questions about the evolution
of plants, scientists still have many more.
Two projects that will continue to develop research from Deep
Green are in the works.
Deep Time will detail the emergence of flowering plants and the
relationship between existing plant families by studying plants'
fossil record and living plants.
Deep Gene will choose plants for complete DNA sequencing.
"It's important to understand these things to understand
life," Waters said. "It's most exciting to know how
things are intertwined."
Advocate staff photo by Bill Feig
Among 200 scientists studying the evolution of green plants, Russell
Chapman, left, looks over magnolia leaves with Debra Waters and
|The Scientist 15:12, March 5, 2001 [top]
'Deep Gene' and 'Deep Time'
Evolving collaborations parse the plant family tree
By Barry A. Palevitz
Amid last month's hoopla over the human genome sequence and what
it says about humans, plant biologists announced two new efforts
aimed at a firmer understanding of plant evolution--who is related
to whom and how--a discipline better known as systematics. Constructing
evolutionary family trees is harder than investigating personal
genealogies--biologists don't have the equivalent of birth registrations
or family bibles to consult. Fossils tell them what ancient plants
use to look like, but placing them in context with living organisms
is difficult at best. Even the systematics of existing plants
can be contentious, as researchers disagree on lumping plants
together or splitting them apart in search of the most natural
Scientists liken constructing phylogenetic trees to tracing all
the branches and trunks of a real tree, like an oak, with only
characteristics of its outermost twigs to go on. That's because
present day organisms are the sole survivors--called "terminals"
by systematists--of multiple, diverging lineages. However daunting
the process, researchers have made breathtaking progress in the
last 20 years, thanks to gene sequencing. According to University
of Georgia systematist David Giannasi, "it was a case of
technology catching up with theory." By comparing DNA sequences
such as those encoding ribosomal RNA and chloroplast proteins,
systematists redrew large chunks of the plant taxonomic map.
A good example of the redefining process is found in the milkweeds,
which taxonomists traditionally placed in a family called the
Asclepiadaceae. They also thought the milkweeds were allied with
a second family, the Apocynaceae. But based on molecular data,
"the Asclepiadaceae nests within the Apocynaceae," says
Giannasi, "so we now know they should be lumped together."
The same is true for the mints, thought to be in their own family
just a few years ago but now grouped with the verbenas.
Researchers have also clarified some of the most basal groups
in the plant family tree. They now know that a previously obscure
New Caledonian shrub called Amborella is sister to all other flowering
plants, or Angiosperms, with water lilies branching off the evolutionary
trunk at the same level or just above.1 They also think the gnetales,
previously considered flowering plant allies, are probably more
closely related to pines, in the Gymnosperms.2 And horsetails
and whisk ferns, once thought to relic descendents of early land
plants, now seem more closely tied to the true ferns.3
Feds Fertilize Interactions
One of the key ingredients in systematists' recipe for success
was cooperation and communication. Thanks to joint funding starting
in 1994 from the U.S. Department of Agriculture, Department of
Energy, and National Science Foundation, a consortium of researchers
called the Green Plant Phylogeny Research Coordination Group,
or Deep Green, pooled ideas and resources in a joint plan of attack.
Machi Dilworth, head of NSF's Division of Biological Infrastructure,
thinks, "Deep Green was one of the very visible success stories"
of the three agency effort. "With a little support they were
able to come together and accomplish major scientific achievements."
NSF was so impressed with the collaborative approach, it decided
to fund "Research Coordination Networks" (RCNs) serving
all areas of the biological sciences. Like Deep Green, the grants
foster communication and collaboration between scientists, but
don't directly cover research costs funded by other programs.
Two of the RCNs are scions of Deep Green.
Systematists Dip Into Genomics
In one of the team projects, called Deep Gene, systematists join
forces with molecular biologists working on entire genomes like
those of Arabidopsis and rice.4,5 By tracing suites of genes that
govern processes such as flower development, they hope to clarify
mechanisms governing major evolutionary changes, including new
biochemical pathways and the appearance of complex morphological
characters. Sequencing also uncovers large-scale genomic changes
including chromosomal rearrangements, which can be invaluable
in defining plant relationships. Likewise, evolution depends on
alteration in spatial and temporal controls governing gene activity--when
and where genes turn on and off. The new RCN hopes to discover
how gene regulation changed in the evolution of various plant
Tolerance toward desiccation is a good example of how traits
may have appeared and disappeared during evolution. The first
plants to occupy dry land faced a big problem compared to their
aquatic ancestors: an uncertain supply of water. Mosses, for example,
grow in moist environments but also suffer periodic drying. That's
why they require biochemical mechanisms that allow them to survive
dry periods. When larger vascular plants arose, with roots and
a plumbing system to extract water from the soil and move it long
distances, desiccation tolerance became less important. But it
reappeared later on in seed plants, which remove water from tissues
surrounding young embryos in preparation for dormancy.
According to Deep Gene principal investigator Brent Mishler of
the University of California at Berkeley--and a veteran of Deep
Green--"around 80 genes are involved in desiccation tolerance
in mosses. When desiccation re-evolved in seeds, some of these
genes were reused." Mishler would like to know how such changes
in gene regulation arose during major evolutionary events. Mishler
chaired a symposium on Deep Green at the annual meeting of the
American Association for the Advancement of Science, February
15-20, in San Francisco.
Daphne Preuss, molecular biologist at the University of Chicago
and Deep Gene co-PI, says she brings to the table "the tools
and techniques of high throughput, big scale biology." Still,
in a true collaboration everybody benefits. With Deep Gene, genomicists
like Preuss want to advance their own projects. In her case, that
means figuring out how centromeres work. Centromeres are DNA sequences
located where chromosomes attach to spindle fibers during mitosis
and meiosis. Preuss has dissected centromeric DNA in Arabidopsis
but knows that "the sequences are very diverse from organism
to organism." The question is, "how did these differences
evolve, and what key components are important for centromere function?"
Adds Preuss," I want insight from looking at conservation
Preuss admits that "this is expensive work, so every decision
counts. We're now making key decisions as to which species to
look at next. We're looking to people in phylogenetics to help."
Mishler sees other practical benefits from Deep Gene. "Can
we use the information for agriculturally important plants that
aren't desiccation tolerant?" he asks. By guiding researchers
to promising sources, Deep Gene can also "predict useful
chemicals for pharmacology," says Mishler. That makes University
of Georgia's Giannasi smile because older studies comparing the
chemical composition of plants--including substances such as terpenoids--predicted
changes cemented by more recent gene sequencing projects. "The
secondary chemistry was there, but nobody trusted it," comments
Fossils and Morphology Join the Fray
Doug and Pamela Soltis of Washington State University in Pullman
lead another RCN called "Deep Time." Having done much
of the gene sequencing for Deep Green, the Soltis' want to superimpose
other kinds of information on their phylogenetic trees, and in
the process add the dimension of time to key points in plant evolution.
Years before systematists accessed gene sequences, they relied
on other information in the form of morphological, anatomical
and chemical characters. While valuable, such characters can be
misleading. For example, a structural trait shared by two groups
could have arisen by convergent evolution rather than common ancestry
(though the same applies to DNA sequences). Moreover, the number
of structural characters applicable to phylogenetic analysis is
limited; DNA sequences, on the other hand, are far more useful
since the average protein encoding sequence contains 1,000-2,000
characters, or nucleotides. That's why they turned to genes.
But the tide may be changing again, at least a little. The Deep
Time RCN will arrange plants according to a "morphological
matrix" of characters, but "constrain the taxa to conform
to the DNA-based topology already available, and in which we have
good confidence at this point," say Pam and Doug Soltis.
They'll then "conduct a phylogenetic analysis of the morphological
matrix with fossils included." The trick will be to pick
characters from existing plants that also apply to fossils. Despite
the fact that "fossils have rarely been integrated in a phylogenetic
context for any group," the Soltis' are hopeful. Since dates
are available for many of the fossils, their inclusion adds a
time factor to the phylogenetic tree--systematists can assign
dates to key branch points. They'll also integrate data from molecular
clocks governed by mutations. "It's sort of like the movie
Back to the Future,'' note the Soltis', "Having the timing
of a key event in the past nailed down is critical in understanding
what has occurred to produce what we see in the present."
The Soltis' also wax philosophical about the collaboration: "We
spent a decade in the area of systematics largely focused on molecules.
There is a wealth of information in nonDNA characters such as
morphology and anatomy, and we can't lose expertise in these areas."
Problems? Cooperation is the Key
Deep Gene and Deep Time researchers realize that reaching their
goals may not be easy. According to the Soltis', "two big
issues are missing data and the combinability of molecular and
morphological data sets." Mishler agrees: "We don't
know entirely how to do it. Theory hasn't kept pace--it's dealt
mostly with sequence data." Researchers hope the latest collaborations
will foster development of new methods to tackle such problems.
Mishler sees promise. "The RCN will help us. Even a small
amount of data from these other sources can improve phylogenetic
trees" and eventually "lead to more research funding."
The depth of cooperation is all the more impressive because deep
Gene and Deep Time will interact.
The "Deep" projects testify to the importance of collaboration
in modern research. According to Doug Soltis, "the cooperative
nature of botanists has really turned the tide in the past decade."
Mishler agrees that "research would have gone on, but it
would not have made the progress it did." Preuss taps federal
agencies for greasing the skids. "Some of these things are
initiated by granting incentives, so I think it's wise. It's good
to stir the pot and mix people together." Adds Machi Dilworth
of NSF, "we would like to foster communication among scientists,
to advance science through collaboration and coordination."
Barry A. Palevitz (firstname.lastname@example.org)
is a contributing editor to The Scientist.
1. B.A. Palevitz, "Discovering
relatives in the flowering plant family tree," The Scientist,
13:12, Dec. 6, 1999.
2. L.M. Bowe et al., "Phylogeny of seed plants based on all
three genomic compartments: extant gymnosperms are monophyletic
and Gnetales' closest relatives are conifers," Proceedings
of the National Academy of Sciences, 97:4092-97, April 11, 2000.
3. K.M. Pryer et al., "Horsetails and ferns are a monophyletic
group and the closest living relatives to seed plants," Nature,
409:618-22, Feb. 2, 2001.
4. B.A. Palevitz, "Arabidopsis
genome. Completed project opens new doors for plant biologists,"
The Scientist, 15:1, Jan. 8, 2001.
5. B.A. Palevitz, "Rice
genome gets a boost," The Scientist, 14:1, May 1,
|Financial Times March 3, 2001 [top]
|BODY AND MIND: Plants that made the leap from the deep: THE NATURE
OF THINGS: A project to unravel the ancestry of today's flora has
produced a surprise, writes Clive Cookson
Financial Times; Mar 3, 2001
By CLIVE COOKSON
Botanists have drawn up the first authoritative "tree of
life" for the plant kingdom. One surprise is the finding
that all land plants are descended from a green alga that emerged
from a lake or river less than 500m years ago.Many scientists
had thought that plants came out of the sea, rather than fresh
water, and that plants successfully invaded the land on more than
The project, known as Deep Green and funded mainly by the US
government, has involved 200 botanists using the latest genetic
techniques to unravel the relationship between today's plants
and their ancestors. Their latest discoveries were described last
week at the American Association for the Advancement of Science
meeting in San Francisco.
The ancestor of all today's land plants, from mosses to ferns,
roses to redwood trees, turns out to be a single-celled green
alga that emerged from fresh water about 470m years ago. That
was 70m years after the great proliferation of invertebrate animals,
including many multicellular creatures, that had taken place in
the oceans during the so-called "Cambrian explosion".
The plants' emergence from the water enabled animals to follow
- first arthropods (the ancestors of insects and spiders) and
then our own vertebrate ancestors. "Animals could not move
on to land until there were some plants there for them to eat,"
says Deep Green project leader Brent Mishler of the University
of California, Berkeley.
Once on land, the plants diversified fast. The ancestors of today's
ferns and horsetails split off from the main lineage of land plants
about 400m years ago. At that time all plants were small, growing
a few centimetres high at most, and they reproduced by spores.
The first trees appeared in the Carboniferous period 300m years
ago. And soon afterwards seeds and pollen evolved, as a more efficient
means of reproduction than simple spores.
But flowers - a further reproductive refinement - did not appear
until about 120m years ago, during the age of dinosaurs. Even
after Deep Green, "the origin of flowers is one of the great
continuing mysteries of plant biology," says Claude de Pamphilis
of Pennsylvania State University.
Flowering plants have the advantage of protecting their seeds
in the fleshy bodies of their fruits - in contrast to more primitive
plants such as conifers that carry "naked seeds". The
closest living relation to the first flowering plants appears
to be an obscure cream-coloured flower called amborella that is
found today only on the South Pacific island of New Caledonia.
The last really important evolutionary step for plants - and
the animals that depend on them - was the appearance of grasses
in the middle of the Tertiary period, about 30m years ago. Grasslands,
which today form important ecological habitats such as savannas,
steppes and prairies, are therefore a relatively recently development.
Within the overall Deep Green story some fascinating strands
of inquiry emerge. Take that first step from water to land. Although
a single lineage of green algae, the charophyceae, gave rise to
all land plants, it turns out that the other three main groups
of green algae conquered the land, too - but they just did not
Russ Chapman, a Deep Green biologist at Louisiana State University,
in Baton Rouge, is particularly interested in the obscure algal
group called trentepohliales, which specialise today in growing
above ground on trees, walls and rooftops. Although these algae
grow mainly in the tropics, they are also common in the damp and
mild conditions of western Ireland, where several species form
orange and red mats on stone and tree bark. (The orange colour
of the carotenoid pigments in the trentepohliales overwhelms the
green of the chlorophyll that is also present.)
Chapman hopes that further research will give some clues about
the reasons why the trentepohliales - which emerged from the sea
rather than fresh water - seem to have hit an evolutionary dead-end.
One of the most important adaptations made by algae to life on
land was to tolerate desiccation. "When plants first invaded
the land, they were all vegetatively tolerant - they could dry
up completely and still be rejuvenated," Mishler says. "But
as plants evolved more complicated structures, they lost this
"The interesting story is that desiccation tolerance re-evolved
at least eight times within flowering plants, and again when the
seed evolved. It appears from our initial work that many of the
genes involved in seed desiccation tolerance are descendants of
the early genes that were involved in vegetative desiccation tolerance
in the first place."
The researchers hope that, if they can understand the group of
genes that enable primitive plants to withstand desiccation, they
will find a way to breed crops that live on less water or survive
Now that Deep Green is drawing to a close, the US National Science
Foundation has agreed to fund two successor projects. The first,
called Deep Time, will explore in greater detail the emergence
of flowering plants and the relationship between existing plant
families, by studying both the fossil record and living plants.
The second project, Deep Gene, will choose the most representative
selection of plants for complete DNA sequencing.
At the same time, the foundation is considering a grander project,
modelled on Deep Green, which would generate a definitive tree
of life for all creatures, including not only plants but also
bacteria and animals.
Copyright: The Financial Times Limited 1995-1998
|Science Online Febuary 19, 2001 [top]
Invasions of the Algae
SAN FRANCISCO--A revised family tree of plants brings surprising
news about how ancient algae moved onto land to give rise to terrestrial
plants--everything from pines to palms to petunias. The conquest
of land happened four different times, researchers said here on
17 February at the annual meeting of the American Association
for the Advancement of Science, ScienceNOW's publisher. But only
one group of invaders successfully diversified into today's land
plants, and it came from a source researchers once considered
unlikely: freshwater lakes or ponds.
Traditionally, biologists thought terrestrial plant life must
have arisen from the oceans. Marine algae, adapted to the salty
sea environment, seemed much better at retaining water than their
freshwater counterparts, and thus at living on land, where dehydration
is a constant threat. Tidepool algae seemed the most likely candidate
predecessors of land plants, but recently, botanists comparing
the anatomy of plants began to suspect that freshwater algae were
the real ancestors.
Researchers collaborating in the international "Deep Green"
project are addressing such questions by putting together a massive
phylogeny, or family tree, of the green plants, based on a comparison
of their genes and phenotypes. Armed with this history book, they
now can trace the evolution of traits through time and across
species. Their tree indicates that all modern land plants are
descendants of a single group of freshwater algae called charophytes.
But the tree also reveals three other, less successful conquests,
Russell Chapman of Louisiana State University told the meeting.
Only one of these originated in saltwater; it gave rise to the
Trentepohliales, a group of 60 species of rock- and tree-hugging
algae that look like orange fuzz.
Why freshwater algae diversified into the 300,000 or so land
plant species that blanket the Earth, while the marine ones never
took off, is unclear. But Chapman suggests that marine invaders,
adapted to saltwater, may face a steep challenge from the freshwater
they'd experience on land in the form of rain. Interestingly,
the algal lineages that moved onto land all share a type of cell
division, called phragomoplastic, that other algae lack, but Chapman
says it's not yet clear how or whether this trait might have aided
a shift onto land.
Rick McCourt, curator of botany at the Academy of Natural Sciences
in Philadelphia, praises the work, but says additional plants
added to the analysis in the future could increase the number
of known invasions of land. Deep Green researchers are now engaged
in "Deep Gene," an attempt to integrate the phylogenetic
data with information from whole genome sequences of plants. This
may allow them to trace the evolution of gene complexes involved
in traits such as desiccation tolerance and cell division, says
Brent Mishler of the University of California, Berkeley--and perhaps
to determine whether groups like the charophytes have special
features that spur diversification.
It came from the sea. Trentepohlia, which grows on bark, is one
of the few terrestrial algae that evolved from saltwater ancestors--but
it was freshwater algae that gave rise to the land plants.
CREDIT: THE AMERICAN PHYTOPATHOLOGICAL SOCIETY
|UC Berkeley Press Release Febuary 16, 2001 [top]
Deep Green spawns Deep Gene and Deep Time to continue work toward
a complete tree of life for the green plants
16 February 2001
By Robert Sanders, Media Relations
San Francisco - The highly successful Deep Green project to construct
a "tree of life" for the green plants has ended, but
it has seeded new projects to strengthen the branches and root
the tree more firmly in new genetic and fossil data.
Among these projects is "Deep Gene," headed by University
of California, Berkeley, botanist Brent D. Mishler, and "Deep
Time," headed by Doug Soltis of the University of Florida.
The National Science Foundation (NSF) has agreed to fund both
projects with $500,000 each over the next five years.
The success of Deep Green also has emboldened NSF to float the
idea of a much larger project - generating the definitive tree
of life for everything, from bacteria to bats, fungi to flowering
plants. NSF director Rita Colwell calls Deep Green one of the
best investments the foundation has made, Mishler said.
Mishler and four colleagues will brief reporters Feb. 16 at 11
a.m. about the accomplishments of Deep Green and its proposed
offshoots. Mishler, a spokesman for Deep Green, is director of
UC Berkeley's University and Jepson Herbaria and a professor of
integrative biology in the College of Letters & Science.
Deep Green has contributed to more than 100 research papers,
Mishler said, the latest of which, in the Feb. 1 issue of Nature,
nailed down the sister group of the seed plants. The work, coauthored
by Kathleen Pryer and Harald Schneider of Chicago's Field Museum
of Natural History and Alan R. Smith and Ray Cranfill of the UC
Berkeley Herbarium, provided very strong evidence that ferns and
horsetails are one another's closest relatives and the group most
closely related to the seed plants.
"It clarifies one big chunk of the tree," Mishler said.
"We haven't completed the whole tree, but these papers one
at a time have dealt with all aspects of the green part of the
tree of life."
The Green Plant Phylogeny Research Coordination Group, initially
funded for a five-year period by the U.S. Department of Energy,
NSF and the Department of Agriculture, was initiated by plant
biologists as a way to make sense of the reams of data on plant
In a series of meetings over the past five years, more than 200
biologists reached consensus on the most important plants to target
in genetic studies and the best genes to focus on. Workshops and
a Web site clearinghouse for phylogenetic information helped the
community of plant biologists coordinate research and answer important
questions about plant relationships.
"It is important to emphasize that this field used to be
very independent and lab-oriented, where everyone was working
in secrecy within the walls of their lab," he said. "But
as a result of Deep Green, people began to cooperate. They started
sharing data and techniques, and that's where this progress came
Among Deep Green's achievements was completion of a good draft
of the tree of life for green plants. It identified a cream-colored
flower called Amborella as the earliest-diverging lineage in the
flowering plants; concluded that land plants first emerged onto
land from fresh water, not the salty oceans; and made clear that,
at many critical transitions in evolution, only one lineage of
green plant survived.
Such information on plant relationships becomes extremely important
as researchers try to engineer new traits -from disease resistance
to drought tolerance - in crop plants.
With Deep Gene, funded through a Research Coordination Networks
grant from NSF, Mishler hopes to repeat the success of Deep Green.
This time, however, he is bringing in scientists working on plant
genomics to reach consensus on the most important plants to target
for genome sequencing.
The genome sequence of the widely-used research plant Arabidopsis
thaliana is nearly complete, and sequencing of the rice and corn
genomes is underway. Genomic data is publicly available on some
19 other plants. To make the most of sequencing efforts, Mishler
said, scientists should choose more diverse plants that cover
the range of economically important land plants.
"You have to pick the landmarks. If you want a good representation
of the whole tree of life, you need to pick genomes nicely spaced
on the tree," he said. "Then, for example, once you
understand the genes involved in flower development in one species,
it's not too difficult to probe for the genes involved in flower
development in nearby species."
He notes that the long-term goal of plant genomics is to identify,
isolate and determine the function of genes associated with various
plant traits. This can be facilitated by a quality tree of life.
Using sister group comparisons, for example, researchers can locate
two closely related plants, one with a particular trait and one
without, to help them reduce the number of genes they need to
look at to isolate those responsible for the trait.
"Ideally, you could narrow the search down to probably just
a few genes from thousands," he said.
Alternatively, ancestor-descendent comparisons allow researchers
to study complex systems of interacting genes, such as those controlling
the angiosperm flower, at a more primitive evolutionary stage,
for example, when they were involved in moss and fern reproduction.
One area where this approach has borne fruit is the study of
dessication tolerance, the ability of plants to withstand drought.
If the trait, common in algae, ferns and lichens, can be transferred
to crop plants, they might subsist on less water or better survive
In a report in last November's Journal of Plant Ecology, Mishler
and U.S. Department of Agriculture researcher Melvin J. Oliver
used sister group comparisons to help unravel this complex phenotype,
which involves more than 80 interacting genes.
"When plants first invaded the land, they were all vegetatively
dessication tolerant - they could dry up completely and still
be rejuvenated. But as plants evolved more complicated structures,
they lost this ability," Mishler said.
"The interesting story is, dessication tolerance re-evolved
at least eight times within flowering plants, and again when the
seed evolved. It appears, from our initial work, that many of
the genes involved in seed dessication tolerance are descendents
of the early genes that were involved in vegetative dessication
tolerance in the first place."
These findings emphasize the value of studying simpler plants
to better understand higher plants, Mishler said.
"We now have real hope that we will be able to understand
something about these economically very important events in evolution,
the evolution of the seed and of the flower, by looking at mosses
and ferns and algae, which are much simpler study systems,"
More insights are sure to come from the interaction between systematists
like Mishler, who chart the evolutionary relationships among plants,
and genomicists identifying the genetic makeup of green plants.
"Deep Gene is an attempt to meld together the plant phylogenetics
progress we've made rapidly in the last few years with the rapid
progress in plant genomics," Mishler said. "We believe
this will be a truly synergistic process, where genomicists and
phylogeneticists both benefit."
|NSF News January 31, 2001 [top]
|Scientists Shake Up "Family Tree" of Green Plants
Apparently, the lowly fern deserves more respect.
New research scheduled to appear as the journal Natures
cover story on February 1 concludes that ferns and horsetails
are not -- as currently believed -- lower, transitional evolutionary
grades between mosses and flowering plants. In fact, ferns and
horsetails, together, are the closest living relatives to seed
"Today's systematists are using genomic tools to re-write
the textbooks on animal and plant evolution," says James
Rodman, program director in NSF's division of environmental biology,
which funded the research. "This research is the latest major
rearrangement of the plant tree of life. It will encourage others
to explore ferns as model organisms for basic ecological and physiological
The research calls for rethinking the "family tree"
of green plants, according to scientists. Also, it uncovers a
research shortcoming: All main plant model organisms used for
research (such as Arabidopsis, which became the first plant to
have all its genes sequenced) are recently evolved flowering plants.
This limitation could compromise scientific research. Models
in the newly identified fern and horsetail lineage are needed
to round out the study of plant development and evolution. This
could help scientists fight invasive species, engineer genetic
traits, develop better crops and prospect the botanical world
The new research uses morphological and DNA sequence data to
show that horsetails and ferns make up one genetically related
group, which evolved in parallel to the other major genetically
related group made up of seed plants and including flowering plants.
"Our discovery that 99 percent of vascular plants fall into
two major lineages with separate evolutionary histories dating
back 400 million years. It will likely have a significant impact
on several disciplines, including ecology, evolutionary biology
and plant developmental genetics," said Kathleen Pryer, lead
author of the paper and assistant curator in botany at The Field
Museum in Chicago. "Viewing these two genetically related
groups as contemporaneous and ancient lineages will likely also
have profound consequences on our understanding of how terrestrial
ecosystems and landscapes evolved."
The work of Pryer and her colleagues builds on the Deep Green
project, a collaboration of researchers dedicated to uncovering
the evolution of and interrelation of all green plants. In 1999,
Deep Green reported at an international botanical conference that
DNA analysis indicates that all green plants -- from the tiniest
single-celled algae to the grandest redwoods -- descended from
a common single-celled ancestor a billion years ago. Green plants,
which include some 500,000 species, are among the best-documented
groups in the tree of life.